Commit 5158d4df authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added start for Shiva report

parent a83aeb9a
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
#{
val fields = List("Hom", "HomVar", "HomRef", "NoCall", "Variant", "NonInformative", "Total")
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
}#
<table>
<thead><tr><th>Sample</th>
#for (field <- fields) <th>${field}</th> #end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
<tr><td>${sample}</td>
#for (field <- fields)
<td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
#end
</tr>
#end
</tbody>
</table>
\ No newline at end of file
package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportPage}
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
/**
* Created by pjvan_thof on 3/30/15.
*/
object ShivaReport extends MultisampleReportBuilder {
def samplePage(sampleId: String, args: Map[String, Any]) = {
ReportPage(Map("Libraries" -> generateLibraryPage(args)), Map(
"Variantcalling" -> "/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"
), args)
}
def libraryPage(libId: String, args: Map[String, Any]) = {
ReportPage(Map("Flexiprep" -> FlexiprepReport.indexPage), Map(), args)
}
def reportName = "Title Test"
def generalPage = ReportPage(Map(), Map(
"Variantcalling" -> "/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp",
"Flexiprep" -> "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepSummary.ssp"
), Map())
// FIXME: Not yet finished
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment